Research workbench
Myosin VI nucleotide-free (MDINSERT2) D179Y crystal structure
Analyse Myosin VI nucleotide-free (MDINSERT2) D179Y crystal structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DBP
- Type
- protein
- Length
- 929 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myosin-VI; Calmodulin
- UniProt
- F1RQI7, P62152
- Ligands
- CA
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myosin-VI | protein | 791 | 50% helix, 16% strand | F1RQI7 |
| C | Calmodulin | protein | 138 | 61% helix, 3% strand | P62152 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains C
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, C
- TBU · Tertiary-butyl alcohol · additive · 2 copies · chains A
- IPA · Isopropyl alcohol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 581 | 0.81 | 0.86 | 85 | TBU, EDO, IPA |
| 2 | 293 | 0.74 | 0.87 | 42 | TBU, EDO |
| 3 | 984 | 0.73 | 0.76 | 72 | empty |
| 4 | 90 | 0.51 | 0.83 | 18 | empty |
| 5 | 236 | 0.51 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–C · 2342 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt F1RQI7
- Every structure of UniProt P62152
- Elsewhere: RCSB PDB 4DBP · PDBe 4DBP · UniProt F1RQI7 · UniProt P62152
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